SMTL ID : 8rdc.1

Galectin-1 in complex with thiogalactoside derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x YNO: 5-bromanyl-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-4-[4-(4-chloranyl-1,3-thiazol-2-yl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-oxan-2-yl]sulfanyl-pyridine-2-carbonitrile(Non-covalent)

YNO.1: 14 residues within 4Å: Chain A: S.30, V.32, H.45, N.47, R.49, H.53, N.62, W.69, G.70, E.72, D.124, G.125 Ligands: GOL.3, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.49, A:N.62 Water bridges: A:R.49, A:R.74 pi-Stacking: A:H.45 Halogen bonds: A:S.30 YNO.8: 13 residues within 4Å: Chain B: S.30, V.32, H.45, N.47, R.49, H.53, N.62, W.69, G.70, E.72, D.124, G.125 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.49, B:N.62, B:E.72 Water bridges: B:N.47, B:R.49 pi-Stacking: B:H.45 Halogen bonds: B:S.30

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.79, Q.81, S.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.84, A:S.84 GOL.3: 8 residues within 4Å: Chain A: V.32, N.34, S.39, L.42, H.45, K.64, W.69 Ligands: YNO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.34, A:S.39 GOL.4: 2 residues within 4Å: Chain A: H.53 Ligands: YNO.1 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain A: N.9, L.10, F.134 Chain B: L.5, I.129 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.9, B:I.129, B:I.129 Water bridges: B:L.5, B:L.5 GOL.9: 7 residues within 4Å: Chain B: V.32, N.34, S.39, H.45, K.64, W.69 Ligands: YNO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.34, B:H.45 Water bridges: B:Y.120

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: D.27, A.28, K.29, D.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.126 SO4.7: 5 residues within 4Å: Chain A: L.5, I.129 Chain B: N.9, L.10, F.134 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:N.9 Hydrogen bonds: A:L.5, A:I.129 Salt bridges: A:K.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hakansson, M. et al., Galectin-1 in complex with thiogalactoside derivative. To Be Published

Release Date

2024-12-18

Peptides

Galectin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galectin-1

Related Entries With Identical Sequence